Mercurial > repos > immuneml > immuneml_tools
diff README.md @ 0:629e7e403e19 draft
"planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
| author | immuneml |
|---|---|
| date | Thu, 01 Jul 2021 11:36:43 +0000 |
| parents | |
| children | ed3932e6d616 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu Jul 01 11:36:43 2021 +0000 @@ -0,0 +1,23 @@ +# immuneml_tools +Galaxy tool wrappers for immuneML. +https://immuneml.uio.no/ + +## Installation: +The tools can be installed from a Galaxy toolshed. You can also install them offline by editing Galaxy config files in the usual way. + +### New datatype `iml_dataset` +No matter how you install the tools, you will need to define a new datatype, which is done as follows: + +1. In your `galaxy.yml` look up the name of your `datatypes_config_file`. If the name is not yet defined, set +``` +datatypes_config_file: datatypes_conf.xml +``` +2. Make `datatypes_conf.xml` by copying `datatypes_conf.xml.sample` unless a `datatypes_config_file` was already defined. +3. Add the following line to your `datatypes_config_file`: +``` +<datatype extension="iml_dataset" type="galaxy.datatypes.text:Html" subclass="True"/> +``` +The line has to be inside `<registration>` along with the other datatypes. + +### The immuneML conda package +Galaxy will need to install the immuneML conda package. This conda installation typically takes several minutes.